Rob Galbraith CompactFlash Performance Databas
is an excellent source of info on two things: Compact Flash in general, and individual cards' actual performance. The database consists of performance timings for dozens of brands and models of CF cards in 1-2 dozen cameras. Unfortunately, all the cameras are DSLRs (probably because they are the only ones - AFAIK - that take advantage of accelerated write speeds). However, there is also a page with timings when writing through a card reader to the computer. This would certainly at least give you an idea of which cards offer generally better or worse performance.
To answer your general question, yes there are differences between brands. However, according to that article, there are only a few companies that manufacture CF card controllers, and only a few companies which manufacture the flash memory used in the cards. The companies who actually market the cards buy each component from one or more of the manufacturers then assembles them together. I didn't notice any indication of whether there's anything that a card manufacturer actually adds, quality wise, to the final product, such as "firmware".
HTH